An experiment was conducted to analyze the favorability of f

An experiment was conducted to analyze the favorability of folding for a short polypeptide consisting entirely of alanine. This polypeptide folds favorably into a single, continuous a-helix. If an individual alanine residue in the polypeptide is changed to glycine, Delta G_ren for the folding of the a-helix increases by +1.88 kcal/mol. In which of the two peptides is a-helix assembly more favorable, the alanine-only peptide or the glycine-containing peptide? Briefly explain your answer. Briefly describe why the substitution of alanine with glycine affects the favorability of a-helix assembly in this way. Your answer must explicitly state whether the difference in favorability is primarily due to a difference in Delat H_xn or a difference in Delat S_ren for the folding of the a-helix. Does the hydrophobic effect contribute significantly to the favorability of a helix assembly for the alanine-only peptide? Assume that the experiment is conducted in a dilute environment such that a-helices do not associate with one another. Briefly explain your answer.

Solution

a)    If deltaG of protein folding is positive that indicates the folding process is unfavorable, If the deltaG is negative ,the folding is favorable,Here the replaced glycines increases the deltaG and hence it is unfavourable.

b)    There are many factors supports the alpha helix stability of alanine rather than glycine,Glycine is too small as compared to alanine and thus unfavourable in alpha helix, the difference in deltaS, that is the entropy is increases that means the polypeptides acquires less ordered form in glycice subdtitutes situation.

c)The hydrophobic effect is more significant in protein folding, the methyl group of Alanine is non-polar ,so in a non-polar environment the entire polypetide gets more ordered structure .